Team:TU-Delft/Timer-Sumo-KillSwitch

From 2013.igem.org

(Difference between revisions)
Line 19: Line 19:
<img src="http://2013.igem.org/wiki/images/8/87/Combined_equations.png" >
<img src="http://2013.igem.org/wiki/images/8/87/Combined_equations.png" >
</center>
</center>
 +
<h2 align="center">Parameters</h2>
<h2 align="center">Parameters</h2>
Line 220: Line 221:
<center>
<center>
<img src="http://2013.igem.org/wiki/images/8/81/Combined.png" width="650" alignment="center">
<img src="http://2013.igem.org/wiki/images/8/81/Combined.png" width="650" alignment="center">
-
<p>Figure 1: Simulation Results</p></div>
+
<p>Figure 1: Simulation Results</p>
</center>
</center>
<br>
<br>
-
<div style="margin-top:10px;margin-left:30px;margin-right:30px;float:left;display:inline-block;"> 
 
<h2 align="center">Conclusion/Discussion</h2>
<h2 align="center">Conclusion/Discussion</h2>
In Figure 1 the behavior of the total circuit is seen, and the answers to the questions can be given:
In Figure 1 the behavior of the total circuit is seen, and the answers to the questions can be given:
Line 234: Line 234:
<h2 align="center">Sensitivity analysis</h2>
<h2 align="center">Sensitivity analysis</h2>
-
To asses the validity of the found answers sensitivity analysis is performed. In this case the numerical derivative of the solution is taken with respect to the parameters of the model. This derivative represents the change of the solution upon changing the specific parameter. If this change is large, the solution is very sensitive for this parameter. Also, since the solution is highly non-linear this numerical derivative is taken in both directions, as they differ greatly in this model.  
+
<p>
-
 
+
To asses the validity of the found answers a sensitivity analysis is performed. In this case the numerical derivative of the solution is taken with respect to the parameters of the model. This derivative represents the change of the solution upon changing the specific parameter. If this change is large, the solution is very sensitive for this parameter. Also, since the solution is highly non-linear this numerical derivative is taken in both directions, as they differ greatly in this model. To compare the found values of the derivative, they are normalized by the nominal value (the solution, e.g. the lyse time). In this way a percentual change is found. Mathematically this can be expressed as:
 +
</p>
 +
<p>
 +
So, for the three answers the sensitivity analysis is done, yielding the follow results and conclusions:
 +
<ol>
 +
<li>The lysis time is not significantly affected by most parameters, only two are important. </li>
 +
</ol>
 +
</p>
 +
</div>
</html>
</html>

Revision as of 08:09, 18 September 2013

Timer-SUMO-KillSwitch


The separate modules: Timer plus SUMO and Kill Switch are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter.

Figure 1: Circuit of the kill switch

Differential Equations

Parameters


Parameter Value Description Units Reference
ca 1020 Translation rate per amino acid min-1#a-1 [7]
cT7 4.16 Maximum transcription rate of T7 #m/min [2]
cptet 2.79 Maximum transcription rate of Ptet #m/min [4]
cpconst 0.5 Transcription rate of Pconst #m/min Assumption
cci 1.79 Maximum transcription rate of Pci #m/min [3]
dmRNA 0.231 Degradation rate of mRNA min-1 [8]
dH 0.0348 Degradation rate of holin / Antiholin M/min [17]
dTET 0.1386 Degradation rate of TET min-1 [9]
dCI 0.042 Degradation rate of CI min-1 [9]
kb,HAH 0.3*10-4 Backward rate [17]
kf,HAH 11.7*10-4 Forward rate [17]
dPEP 2.1*10-3 Degradation rate of the peptide min-1 Assumed three times slower same as GFP
dPSU 6.3*10-3 Degradation rate of the peptide plus SUMO min-1 Assumed the same as GFP
dUlp 1.263*10-2 Degradation rate of Ulp min-1 Assumed twice the rate of GFP
lt7 0.002 Leakage factor of T7 - Assumption
lptet 0.002 Leakage factor of Ptet - Assumption
lci 0.002 Leakage factor of Pci - Assumption
ktet 6 Dissociation constant of Ptet #m [10]
kci 20 Dissociation constant of Pci #m [10]
kcUlp 3 Turnover rate of Ulp min-1 [6]
nci 3 Hills coefficient - [11]
ntet 3 Hills coefficient - [11]
s 0 or 1 Activation/Inactivation of T7 promoter Binary Assumption
sci 228 Length of CI amino acids [12]
sPSU 18 + 110 Length of peptide plus SUMO amino acids [12]
sTET 206 Length of TET amino acids [13]
sUlp 233 Length of Ulp1 amino acids [13]
sH 219 Length of Holin amino acids
sAH 103 Length of Antiholin amino acids


Results

In Figure 1 the results of the simulation are shown.

Figure 1: Simulation Results


Conclusion/Discussion

In Figure 1 the behavior of the total circuit is seen, and the answers to the questions can be given:
  1. How much peptides are produced by the circuit?
    The total concentration is 18000 peptides per cell.
  2. How much peptides are still uncleaved by the SUMO at the point of cell lysis?
    The models shows that there is almost no SUMO-peptide uncleaved.
  3. How many minutes does the cell lysis take from the point of induction?
    After 165 minutes the Holin concentration passes 190 molecules per cell and cell lysis occurs.

Sensitivity analysis

To asses the validity of the found answers a sensitivity analysis is performed. In this case the numerical derivative of the solution is taken with respect to the parameters of the model. This derivative represents the change of the solution upon changing the specific parameter. If this change is large, the solution is very sensitive for this parameter. Also, since the solution is highly non-linear this numerical derivative is taken in both directions, as they differ greatly in this model. To compare the found values of the derivative, they are normalized by the nominal value (the solution, e.g. the lyse time). In this way a percentual change is found. Mathematically this can be expressed as:

So, for the three answers the sensitivity analysis is done, yielding the follow results and conclusions:

  1. The lysis time is not significantly affected by most parameters, only two are important.